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JMP Clinical _ Adverse Event detection based on CTCAE grade

What inspired this Wish List Request? 

When clinical data monitoring, clinicians  collect many lab results. Checking if adverse events (AEs) have been properly reported according to the CTCAE grade based on lab values, and cross-checking AEs and labs is a very time-consuming task. Conversely, there are cases where AEs are reported, but the related lab values are either not reported or normal. Therefore, having a report that can crosscheck these things during the clinical data monitoring process would be really helpful.

Please describe the new or improved feature or solution you would like to see. 

same as above 

 

What would the value be to you and/or other users if this new feature is provided? 

Time saving for cleaning data monitoring, ensure data integrity

Is this an external customer request? 

No, It is the needs from my industry experience

Is there a competitive software package that has this feature or solution that we should be aware of? 

I don't know. when i was in pharma, it was a very sas-programming, highly manual review tasks. 

 

Will this impact a renewal, expansion, or adoption at a customer, and does this put an account at risk if we do not address this? 

 

Content OrganizationRe: JMP Clinical _ Adverse Event detection based on CTCAE grade

@andreacoombs1 and I have see this request before. We created a crude script/JMP Clinical report to do something like this. I think it was BMS that requested this report as well.

 /*
 Authors:
	Andrea Coombs and Chris Kirchberg, JMP Statistical Discovery, LLC
 
 Subject:
	CTC Grade Adjudication Report based on DM, AE and LB domain data
	ADaM version has yet to be confirmed
 
 Summary:

 
 Original Date of Creation:
	May 5th, 2023
 
 Original JMP Clinical Target Version:
	17.2
 
  Updated:
	May 5th, 2023

Current Report Version:
	1.1
 
 Current JMP Clinical Target Version:
	17.2
*/

Names Default To Here( 1 );

/*
	Define the report to the report selector with the following attributes:
	label, reportSelectorTab, drillDown, cdiscClass, icon and documentation
*/
processNS:label = "CTC Grade Adjudication";
processNS:reportSelectorTab = 1;
processNS:drillDown = 0;
processNS:cdiscClass = locale:get( "OtherEvents_Text" );
processNS:icon = "/install/clinical/documentation/icons/clinical/bar_chart_16p.png"; //Location/path for custom icon
processNS:documentation = jg:getReportHelpPath(); //Place holder for location of documentation/Help

//This will be called at report selection time to see if the report is supported
//The objRefNS object does not exist yet
//Definging required domains and variables
processNS:requirements = ["AE" => {{"USUBJID", "AEBODSYS", "AETOXGR", "AESTDY", "AEENDY", "AETERM"}, {"_ALL_"}}, "LB" => {{"USUBJID", "LBTEST",
"LBSTRESN", "LBDY"}, {"_ALL_"}}];

//Function to run report when adding report to review template with main code inside
processNS:runReport = Function( {},
	{Default Local}, 
	
	//Required to use loadData,....
	Include( Convert File Path( "$CLINICAL_HOME/JSLFiles/DataPrep.JSL", absolute, windows ) );

	//Get/load AE and LBdomain and set a reference to it.
	
	objRefNS:aeDT = loadData( "AE" );
	objRefNS:lbDT = loadData( "LB" );	

// Clear row selection
	objRefNS:aeDT << Clear Select;

// Subset data table
	// → Data Table( "Subset of ae" )
	objRefNS:subAEDT = objRefNS:aeDT << Select Where( :AEBODSYS == "BLOOD AND LYMPHATIC SYSTEM DISORDERS" | :AEBODSYS == "INVESTIGATIONS" ) <<
	Subset( Invisible, Selected Rows( 1 ), Selected columns only( 0 ) );


// Close Data Table: ae
	Close( objRefNS:aeDT, NoSave );

// Subset data table
	// → Data Table( "Subset of lb" )
	objRefNS:subLBDT = objRefNS:lbDT << Select Where( :LBTEST == "Hemoglobin" | :LBTEST == "Platelet" ) << Subset(
		Invisible,
		Selected Rows( 1 ),
		Selected columns only( 0 )
	);

// Close Data Table: lbx
	Close( objRefNS:lbDT, NoSave );
	
// Split data table
	// → Data Table( "Split LB" )
	objRefNS:splitLBDT = objRefNS:subLBDT << Split(
		Split By( :LBTEST ),
		Split( :LBSTRESN ),
		Group( :USUBJID, :LBDY ),
		Output Table( "Split LB" ),
		Remaining Columns( Drop All ),
		Sort by Column Property,
		Invisible
	);
// Close Data Table: Subset of lb
	Close( objRefNS:subLBDT, NoSave );

// New column: CTC Grade
	objRefNS:splitLBDT << New Column( "CTC Grade",
		Character,
		"Nominal",
		Formula(
			If( !Is Missing( :Hemoglobin ) & !Is Missing( :Platelet ),
				If(
					:Hemoglobin > 17 | :Platelet > 600, 3,
					15 < :Hemoglobin <= 17 | 400 < :Platelet <= 600, 2,
					1
				),
				If( !Is Missing( :Hemoglobin ),
					If(
						:Hemoglobin > 17, 3,
						15 < :Hemoglobin <= 17, 2,
						1
					),
					If(
						:Platelet > 600, 3,
						400 < :Platelet <= 600, 2,
						1
					)
				)
			)
		)
	);


// Change column name: AETOXGR → CTC Grade
	objRefNS:subAEDT:AETOXGR << Set Name( "CTC Grade" );


// Concatenate tables
	// → Data Table( "CTC Grade Judication" )
	objRefNS:ctcGrdAdDT = objRefNS:subAEDT << Concatenate( Invisible, objRefNS:splitLBDT, Output Table( "CTC Grade Adjudication" ) );

// Close Data Table: split of subset of lb
	Close( objRefNS:splitLBDT, NoSave );
	
// Close Data Table: subset of ae
	Close( objRefNS:subAEDT, NoSave );
	
//Link demography data to CTC Grade Adjudication table
	report:linkAnalysisTableToADSLTable( objRefNS:ctcGrdAdDT );

	processNS:setReportOutput(
		objRefNS:resultsContainer = V List Box(
				
			objRefNS:outBox1 = Outline Box( "Results", 
			// Report snapshot: CTC Grade Adjudication - Graph Builder
				objRefNS:gb1 = objRefNS:ctcGrdAdDT << Graph Builder(
					Size( 518, 714 ),
					Show Control Panel( 0 ),
					Variables(
						X( :AESTDY ),
						X( :AEENDY, Position( 1 ) ),
						X( :LBDY, Position( 1 ) ),
						Y( :AETERM ),
						Y( :Hemoglobin ),
						Y( :Platelet ),
						Color( :CTC Grade )
					),
					Elements( Position( 1, 1 ), Points( X( 1 ), X( 2 ), Y, Legend( 23 ) ) ),
					Elements( Position( 1, 2 ), Line( X( 3 ), Y, Legend( 27 ) ), Points( X( 3 ), Y, Legend( 29 ) ) ),
					Elements( Position( 1, 3 ), Line( X( 3 ), Y, Legend( 26 ) ), Points( X( 3 ), Y, Legend( 28 ) ) ), 
/*					Local Data Filter(
						Add Filter( columns( :USUBJID ), Where( :USUBJID == "21031" ), Display( :USUBJID, N Items( 15 ), Find( Set Text( "" ) ) ) )
					),*/
					SendToReport(
						Dispatch(
							{},
							"400",
							ScaleBox,
							{Legend Model(
								23,
								Properties( 0, {Line Color( 4 )}, Item ID( "1", 1 ) ),
								Properties( 1, {Line Color( 9 )}, Item ID( "2", 1 ) ),
								Properties( 2, {Marker( "Filled Right Triangle" )}, Item ID( "AESTDY", 1 ) ),
								Properties( 3, {Marker( "Filled Left Triangle" )}, Item ID( "AEENDY", 1 ) ),
								Properties( -1, {Line Color( 3 )}, Item ID( "3", 1 ) )
							), Legend Model(
								27,
								Properties( 0, {Line Color( 32 )}, Item ID( "1", 1 ) ),
								Properties( 1, {Line Color( 32 )}, Item ID( "2", 1 ) ),
								Properties( -1, {Line Color( 32 )}, Item ID( "3", 1 ) )
							), Legend Model(
								29,
								Base( 0, 0, 0, Item ID( "1", 1 ) ),
								Base( 1, 0, 1, Item ID( "2", 1 ) ),
								Properties( 0, {Line Color( 4 )}, Item ID( "1", 1 ) ),
								Properties( 1, {Line Color( 9 )}, Item ID( "2", 1 ) ),
								Base( -1, 0, 2, Item ID( "3", 1 ) ),
								Properties( -1, {Line Color( 3 )}, Item ID( "3", 1 ) )
							), Legend Model(
								26,
								Base( 0, 0, 0, Item ID( "1", 1 ) ),
								Base( 1, 0, 1, Item ID( "2", 1 ) ),
								Properties( 0, {Line Color( 32 )}, Item ID( "1", 1 ) ),
								Properties( 1, {Line Color( 32 )}, Item ID( "2", 1 ) ),
								Base( -1, 0, 2, Item ID( "3", 1 ) ),
								Properties( -1, {Line Color( 32 )}, Item ID( "3", 1 ) )
							), Legend Model(
								28,
								Base( 0, 0, 0, Item ID( "1", 1 ) ),
								Base( 1, 0, 1, Item ID( "2", 1 ) ),
								Properties( 0, {Line Color( 4 )}, Item ID( "1", 1 ) ),
								Properties( 1, {Line Color( 9 )}, Item ID( "2", 1 ) ),
								Base( -1, 0, 2, Item ID( "3", 1 ) ),
								Properties( -1, {Line Color( 3 )}, Item ID( "3", 1 ) )
							)}
						),
						Dispatch(
							{},
							"400",
							LegendBox,
							{Legend Position( {23, [0, 1, 2, 3], 27, [-1, -1], 29, [-1, -1], 26, [-1, -1], 28, [-1, -1]} )}
						)
					)
				)
			)
		)
	);
	//Display data tables created or used in this report
	processNS:addDataTableReference( "CTC Grade Adjudication Table", "objRefNS:ctcGrdAdDT" );

);

// return code
0;

Re: JMP Clinical _ Adverse Event detection based on CTCAE grade

Oh, @Chris_Kirchberg  This Report was already requested and developed before. Sounds good. Hope this reports be integrated soon. And Thank you for sharing the JSL! 

Re: JMP Clinical _ Adverse Event detection based on CTCAE grade

This feature is beneficial as it streamlines the clinical data monitoring process, which is crucial when clinicians are handling numerous lab results. Ensuring that adverse events (AEs) are reported accurately according to CTCAE grades based on lab values is essential but time-consuming. Sometimes, AEs are reported without corresponding lab values or with normal values, adding complexity. Introducing a report that can cross-check AEs and lab values will save significant time and improve the accuracy and reliability of clinical trials. Additionally, many of our customers currently resort to custom coding to manage these issues, so an out-of-the-box solution would be favorable.

Re: JMP Clinical _ Adverse Event detection based on CTCAE grade - Status changed to: AcknowledgedRe: JMP Clinical _ Adverse Event detection based on CTCAE grade

Thank you for the idea!  I think this is an interesting idea to add to Clinical.  I need to do a little research to see how feasible it would be to identify which AEs and lab tests should be used and paired to make this generic.